All File Changes

v421_preview to v421_preview2 (2021-09-13 to 2021-09-20) v421

• confs/asia.hg.conf
  • lines changed 9, context: html, text, full: html, text
    ec3600bf45f78d2e199220628ea8ce908c3c5923 Sun Sep 19 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 9, context: html, text, full: html, text
    ec3600bf45f78d2e199220628ea8ce908c3c5923 Sun Sep 19 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 14, context: html, text, full: html, text
    ec3600bf45f78d2e199220628ea8ce908c3c5923 Sun Sep 19 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/preview.hg.conf
  • lines changed 3, context: html, text, full: html, text
    ec3600bf45f78d2e199220628ea8ce908c3c5923 Sun Sep 19 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 9, context: html, text, full: html, text
    ec3600bf45f78d2e199220628ea8ce908c3c5923 Sun Sep 19 01:11:43 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGene.c
  • lines changed 6, context: html, text, full: html, text
    f7e3242e7ed1ccf7c353e547312e76fd85112a47 Mon Sep 13 16:06:14 2021 -0700
    some tweaks to the knownGeneArchive
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 73, context: html, text, full: html, text
    f22f0b5f1d467e570dad2407813748889408d9bd Tue Sep 14 09:38:11 2021 -0700
    Don't rely on outputs printed only when usher is compiled with -DDEBUG=1; those are going away in server mode. We already weren't showing the 'Best nodes' output, so just remove that code. We already have sample mutations in seqInfo->sncList, so just reformat that into placementInfo->sampleMuts.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 12, context: html, text, full: html, text
    f22f0b5f1d467e570dad2407813748889408d9bd Tue Sep 14 09:38:11 2021 -0700
    Don't rely on outputs printed only when usher is compiled with -DDEBUG=1; those are going away in server mode. We already weren't showing the 'Best nodes' output, so just remove that code. We already have sample mutations in seqInfo->sncList, so just reformat that into placementInfo->sampleMuts.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 104, context: html, text, full: html, text
    f22f0b5f1d467e570dad2407813748889408d9bd Tue Sep 14 09:38:11 2021 -0700
    Don't rely on outputs printed only when usher is compiled with -DDEBUG=1; those are going away in server mode. We already weren't showing the 'Best nodes' output, so just remove that code. We already have sample mutations in seqInfo->sncList, so just reformat that into placementInfo->sampleMuts.
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 2, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 11, context: html, text, full: html, text
    ddde745372e6f9aa3cb0d4e4fde7bece33eafa2e Thu Sep 16 13:32:49 2021 -0700
    Adding closing tags and breaks that were missing
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/FAQ/index.html
  • lines changed 14, context: html, text, full: html, text
    507780a3f59aa379d0f02adcc94750a1eba11637 Tue Sep 14 13:57:19 2021 -0700
    moved search boxes into empty space above the fold
  • lines changed 14, context: html, text, full: html, text
    5e8c9f2156d62cb534d658c39b11a1cdf17e8a76 Thu Sep 16 17:56:15 2021 -0700
    Revert "moved search boxes into empty space above the fold" This reverts commit 507780a3f59aa379d0f02adcc94750a1eba11637.
  • lines changed 14, context: html, text, full: html, text
    d588e86921ab039bcd59cce5c1d8b5ba4bdd59f1 Thu Sep 16 17:59:56 2021 -0700
    Revert "Revert "moved search boxes into empty space above the fold"" This reverts commit 5e8c9f2156d62cb534d658c39b11a1cdf17e8a76.
• src/hg/htdocs/contacts.html
  • lines changed 2, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    ef46bffc08cc131f944ee1b8f96465e60aeb5a29 Thu Sep 16 17:57:50 2021 -0700
    clarified the meaning a bit per jonathan suggestion. refs #28158
  • lines changed 1, context: html, text, full: html, text
    29a517aaa5dfc20c2136ee582f36a000b93523b7 Thu Sep 16 18:04:08 2021 -0700
    small change to wording
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 6, context: html, text, full: html, text
    aabaeabcd0ff25b35909e747ff24714885b07490 Wed Sep 15 14:18:27 2021 -0700
    Adding links to the new blog about sessions in session help pages refs #27945
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 3, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 1, context: html, text, full: html, text
    5e00cd8a9a64cbb632e6b77adb3c634160e97742 Thu Sep 16 15:25:20 2021 -0700
    Fixing insecure form messages refs #28175
  • lines changed 1, context: html, text, full: html, text
    63130a0a315c1c10d58d741cdf534d922cece886 Thu Sep 16 15:44:09 2021 -0700
    Adding S to http to eliminate warning when searching docs refs #28175
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 3, context: html, text, full: html, text
    aabaeabcd0ff25b35909e747ff24714885b07490 Wed Sep 15 14:18:27 2021 -0700
    Adding links to the new blog about sessions in session help pages refs #27945
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    1ebfdf9a14d79221b7c27b932f7b0596c876755f Wed Sep 15 16:36:00 2021 -0700
    Updating news for cactus 241-way alignment track, refs #27519
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    1ebfdf9a14d79221b7c27b932f7b0596c876755f Wed Sep 15 16:36:00 2021 -0700
    Updating news for cactus 241-way alignment track, refs #27519
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    46c61387f4099587f4c891f0d9ca430afd48cc6d Tue Sep 14 13:17:05 2021 -0700
    updating workshop list. adding open house annoucement
• src/hg/htdocs/training/openHouse.html
  • lines changed 46, context: html, text, full: html, text
    46c61387f4099587f4c891f0d9ca430afd48cc6d Tue Sep 14 13:17:05 2021 -0700
    updating workshop list. adding open house annoucement
• src/hg/inc/botDelay.h
  • lines changed 17, context: html, text, full: html, text
    057858d2b2362378236155cfe531f6b5850df195 Wed Sep 15 15:24:29 2021 -0700
    no botDelay sleep until over warnMs and remove dead code refs #28173
  • lines changed 16, context: html, text, full: html, text
    c14f04a77954e2abf3747d2943c42e4a499d0f6b Mon Sep 20 10:03:35 2021 -0700
    restore obsolete botDelay code required by hgPhyloPlace and do not set variables that are in environment
• src/hg/inc/trackDb.h
  • lines changed 2, context: html, text, full: html, text
    a469233b735071329c483e7c850956ec12f937a1 Wed Sep 15 17:21:55 2021 -0700
    be smarter about checking to see if users are specifying a filter on the same field in different ways
• src/hg/lib/botDelay.c
  • lines changed 70, context: html, text, full: html, text
    057858d2b2362378236155cfe531f6b5850df195 Wed Sep 15 15:24:29 2021 -0700
    no botDelay sleep until over warnMs and remove dead code refs #28173
  • lines changed 67, context: html, text, full: html, text
    c14f04a77954e2abf3747d2943c42e4a499d0f6b Mon Sep 20 10:03:35 2021 -0700
    restore obsolete botDelay code required by hgPhyloPlace and do not set variables that are in environment
• src/hg/lib/hui.c
  • lines changed 34, context: html, text, full: html, text
    a469233b735071329c483e7c850956ec12f937a1 Wed Sep 15 17:21:55 2021 -0700
    be smarter about checking to see if users are specifying a filter on the same field in different ways
  • lines changed 1, context: html, text, full: html, text
    c866e01c54a12052427cac0ade916a4707ff04f2 Thu Sep 16 15:51:28 2021 -0700
    Remove reliance on hg.conf for printing related tracks section for hgTrackUi and hgc, refs #27550
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 32, context: html, text, full: html, text
    515fcc033a455f3e44a1d3c6766ae620738f53f3 Wed Sep 15 16:39:52 2021 -0700
    Updating description.html for hg38 for patch13 release.
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 42, context: html, text, full: html, text
    f7e3242e7ed1ccf7c353e547312e76fd85112a47 Mon Sep 13 16:06:14 2021 -0700
    some tweaks to the knownGeneArchive
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.html
  • lines changed 2, context: html, text, full: html, text
    d2c1321c9c3ff10cce39541479ea5c0ef71cc00a Thu Sep 16 13:31:18 2021 -0700
    Adding missing closing tags
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    df9ebd94831493d052e13311c84c9541bff9e984 Fri Sep 17 11:37:57 2021 -0700
    Adding linkouts and updating desc page for MANE refs #28141
  • lines changed 20, context: html, text, full: html, text
    acdb2bd6a726a7dac4555099f8f6a9be19a1326e Fri Sep 17 14:52:27 2021 -0700
    Releading MANE v0.95 update refs #28141
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 1, context: html, text, full: html, text
    a86b30e920a1a7e373d7c0da353e8325b863f8a0 Wed Sep 15 13:43:04 2021 -0700
    Adding missing tag from CR refs #28160
  • lines changed 3, context: html, text, full: html, text
    df9ebd94831493d052e13311c84c9541bff9e984 Fri Sep 17 11:37:57 2021 -0700
    Adding linkouts and updating desc page for MANE refs #28141
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 8, context: html, text, full: html, text
    acdb2bd6a726a7dac4555099f8f6a9be19a1326e Fri Sep 17 14:52:27 2021 -0700
    Releading MANE v0.95 update refs #28141
• src/hg/makeDb/trackDb/human/hg38/oldKnownGene.ra
  • lines changed 41, context: html, text, full: html, text
    f7e3242e7ed1ccf7c353e547312e76fd85112a47 Mon Sep 13 16:06:14 2021 -0700
    some tweaks to the knownGeneArchive
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f7e3242e7ed1ccf7c353e547312e76fd85112a47 Mon Sep 13 16:06:14 2021 -0700
    some tweaks to the knownGeneArchive
  • lines changed 2, context: html, text, full: html, text
    acdb2bd6a726a7dac4555099f8f6a9be19a1326e Fri Sep 17 14:52:27 2021 -0700
    Releading MANE v0.95 update refs #28141
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 4, context: html, text, full: html, text
    aa80667780417df15ea62d143ac4c3ea8b5e9f8f Mon Sep 13 15:47:29 2021 -0700
    Minor tweaks to JASPAR html refs #27061
• src/hg/makeDb/trackDb/knownGeneArchive.html
  • lines changed 4, context: html, text, full: html, text
    f7e3242e7ed1ccf7c353e547312e76fd85112a47 Mon Sep 13 16:06:14 2021 -0700
    some tweaks to the knownGeneArchive
• src/hg/utils/otto/lrg/bigPsl+6.as
  • lines changed 1, context: html, text, full: html, text
    f0527b030e6164ea3bf58446dfaef6da1d4f62dd Tue Sep 14 10:41:07 2021 -0700
    Fix lrg build to not depend on checked out copy of kent source, copy all scripts locally
• src/hg/utils/otto/lrg/buildLrg.sh
  • lines changed 7, context: html, text, full: html, text
    f0527b030e6164ea3bf58446dfaef6da1d4f62dd Tue Sep 14 10:41:07 2021 -0700
    Fix lrg build to not depend on checked out copy of kent source, copy all scripts locally
• src/hg/utils/otto/lrg/makefile
  • lines changed 6, context: html, text, full: html, text
    f0527b030e6164ea3bf58446dfaef6da1d4f62dd Tue Sep 14 10:41:07 2021 -0700
    Fix lrg build to not depend on checked out copy of kent source, copy all scripts locally
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    2d5070b9ab117f4f66ab71c268d7c130291a0ec8 Mon Sep 20 10:12:27 2021 -0700
    v421 preview2, refs #28170

• lines changed: 805
• files changed: 62